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- PDB-8qck: Crystal structure of mycothiol disulfide reductase Mtr from Mycob... -

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Basic information

Entry
Database: PDB / ID: 8qck
TitleCrystal structure of mycothiol disulfide reductase Mtr from Mycobacterium smegmatis
ComponentsPyridine nucleotide-disulfide oxidoreductase dimerization region
KeywordsOXIDOREDUCTASE / DISULFIDE REDUCTASE / FLAVOPROTEIN / MYCOTHIONE REDUCTASE
Function / homology
Function and homology information


Oxidoreductases; Acting on a sulfur group of donors; With NAD+ or NADP+ as acceptor / oxidoreductase activity, acting on a sulfur group of donors, NAD(P) as acceptor / flavin adenine dinucleotide binding
Similarity search - Function
Mycothione reductase / Pyridine nucleotide-disulphide oxidoreductase, class I / Pyridine nucleotide-disulphide oxidoreductase, class I, active site / Pyridine nucleotide-disulphide oxidoreductases class-I active site. / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / FAD/NAD-linked reductase, dimerisation domain superfamily / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Pyridine nucleotide-disulfide oxidoreductase dimerization region
Similarity search - Component
Biological speciesMycolicibacterium smegmatis MC2 155 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.7 Å
AuthorsGutierrez-Fernandez, J. / Hammerstad, M. / Hersleth, H.-P.
Funding support Norway, 1items
OrganizationGrant numberCountry
Research Council of Norway144971 Norway
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2024
Title: The crystal structure of mycothiol disulfide reductase (Mtr) provides mechanistic insight into the specific low-molecular-weight thiol reductase activity of Actinobacteria.
Authors: Gutierrez-Fernandez, J. / Hersleth, H.P. / Hammerstad, M.
History
DepositionAug 27, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 13, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pyridine nucleotide-disulfide oxidoreductase dimerization region
B: Pyridine nucleotide-disulfide oxidoreductase dimerization region


Theoretical massNumber of molelcules
Total (without water)99,9982
Polymers99,9982
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6580 Å2
ΔGint-38 kcal/mol
Surface area36760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.959, 209.563, 241.871
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1chain "B"

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: GLU / End label comp-ID: GLU / Auth seq-ID: 1 - 461 / Label seq-ID: 1 - 461

Dom-IDAuth asym-IDLabel asym-ID
d_1AA
d_2BB

NCS oper: (Code: givenMatrix: (-0.979197738181, -0.00656999600635, 0.202801934641), (0.00495677867763, -0.999951915315, -0.00846152490312), (0.202847775158, -0.00728026174129, 0.979183219782)Vector: ...NCS oper: (Code: given
Matrix: (-0.979197738181, -0.00656999600635, 0.202801934641), (0.00495677867763, -0.999951915315, -0.00846152490312), (0.202847775158, -0.00728026174129, 0.979183219782)
Vector: 12.1014999829, -127.22916845, -1.90739826155)

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Components

#1: Protein Pyridine nucleotide-disulfide oxidoreductase dimerization region


Mass: 49998.836 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis MC2 155 (bacteria)
Gene: gorA, MSMEI_2549 / Production host: Escherichia coli (E. coli)
References: UniProt: I7G0D4, Oxidoreductases; Acting on a sulfur group of donors; With NAD+ or NADP+ as acceptor

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.3 Å3/Da / Density % sol: 62.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.02 M magnesium chloride hexahydrate, 0.1 M HEPES pH 7.5 and 22% (w/v) poly-(acrylic acid sodium salt) 5,100, and a protein concentration of 12.5 mg/mL.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9184 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Oct 5, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 4.7→49.4 Å / Num. obs: 7284 / % possible obs: 99.9 % / Redundancy: 6.1 % / Biso Wilson estimate: 55.63 Å2 / CC1/2: 0.942 / Rmerge(I) obs: 0.635 / Rpim(I) all: 0.278 / Rrim(I) all: 0.695 / Net I/σ(I): 3
Reflection shellResolution: 4.7→5.25 Å / Redundancy: 6.3 % / Rmerge(I) obs: 1.183 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2015 / CC1/2: 0.847 / Rpim(I) all: 0.514 / Rrim(I) all: 1.292 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8QCJ

8qcj


Resolution: 4.7→49.37 Å / SU ML: 0.8538 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 41.1901
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3384 710 9.98 %
Rwork0.2925 6403 -
obs0.2972 7113 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 113.65 Å2
Refine analyzeLuzzati coordinate error obs: 1.243 Å
Refinement stepCycle: LAST / Resolution: 4.7→49.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7036 0 0 0 7036
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00337172
X-RAY DIFFRACTIONf_angle_d0.82619760
X-RAY DIFFRACTIONf_chiral_restr0.04861118
X-RAY DIFFRACTIONf_plane_restr0.00631286
X-RAY DIFFRACTIONf_dihedral_angle_d6.03171004
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.39684432767 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.7-5.060.38291370.29631206X-RAY DIFFRACTION96.07
5.06-5.570.40071370.32941237X-RAY DIFFRACTION97.1
5.57-6.370.45281310.33471282X-RAY DIFFRACTION97.38
6.38-8.020.34341320.32381304X-RAY DIFFRACTION99.38
8.03-49.370.26061730.23851374X-RAY DIFFRACTION99.61

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